/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.sam;
import org.broad.igv.feature.BasicFeature;
import org.broad.igv.feature.Exon;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.feature.Strand;
import org.broad.igv.track.WindowFunction;
import java.awt.*;
import java.util.List;
/**
* Some alignment formats are parsed as Features.
* <p/>
* This is all getting rather circular, some refactoring is in order.
*
* @author jrobinso
* @date Aug 5, 2010
*/
public class FeatureWrappedAlignment implements Alignment {
String readName;
String chr;
int start;
int end;
AlignmentBlockImpl[] blocks;
Strand strand;
public FeatureWrappedAlignment(BasicFeature f) {
this.readName = f.getName();
this.chr = f.getChr();
this.start = f.getStart();
this.end = f.getEnd();
strand = f.getStrand();
if (f.getExonCount() > 0) {
blocks = new AlignmentBlockImpl[f.getExonCount()];
int i = 0;
for (Exon exon : f.getExons()) {
int length = exon.getLength();
byte[] seq = new byte[length];
blocks[i] = new AlignmentBlockImpl(exon.getStart(), seq, seq);
i++;
}
}
}
public String getReadName() {
return readName;
}
public String getReadSequence() {
return null;
}
public String getChromosome() {
return chr;
}
public String getChr() {
return chr;
}
@Override
public String getContig() {
return chr;
}
public int getAlignmentStart() {
return start;
}
public boolean contains(double location) {
return location >= start && location <= getEnd();
}
public AlignmentBlock[] getAlignmentBlocks() {
return blocks;
}
public AlignmentBlock[] getInsertions() {
return null;
}
public String getCigarString() {
return "*";
}
public int getInferredInsertSize() {
return 0;
}
public int getMappingQuality() {
return 255;
}
public ReadMate getMate() {
return null;
}
public boolean isProperPair() {
return true;
}
public boolean isMapped() {
return true;
}
public boolean isPaired() {
return false;
}
public boolean isNegativeStrand() {
return strand == Strand.NEGATIVE;
}
public boolean isDuplicate() {
return false;
}
public float getScore() {
return 1.0f;
}
public LocusScore copy() {
return this;
}
public String getClipboardString(double location, int mouseX) {
return getValueString(location, mouseX, null);
}
public String getValueString(double position, int mouseX, WindowFunction windowFunction) {
return readName + "<br>Read length = " + (getEnd() - getStart());
}
/**
* @return the start
*/
public int getStart() {
return start;
}
/**
* @param start the start to set
*/
public void setStart(int start) {
this.start = start;
}
/**
* @return the end
*/
public int getEnd() {
return end;
}
public int getAlignmentEnd() {
return end;
}
/**
* @param end the end to set
*/
public void setEnd(int end) {
this.end = end;
}
public byte getBase(double position) {
return 0;
}
public byte getPhred(double position) {
return 0;
}
public String getSample() {
return null;
}
public String getReadGroup() {
return null;
}
public String getLibrary() {
return null;
}
public Object getAttribute(String key) {
return null; //To change body of implemented methods use File | Settings | File Templates.
}
public void setMateSequence(String sequence) {
//To change body of implemented methods use File | Settings | File Templates.
}
public String getPairOrientation() {
return null; //To change body of implemented methods use File | Settings | File Templates.
}
public boolean isSmallInsert() {
return false; //To change body of implemented methods use File | Settings | File Templates.
}
public boolean isVendorFailedRead() {
return false; //To change body of implemented methods use File | Settings | File Templates.
}
public Color getColor() {
return null;
}
@Override
public List<Gap> getGaps() {
return null;
}
public boolean isFirstOfPair() {
return false;
}
public boolean isSecondOfPair() {
return false;
}
public Strand getFirstOfPairStrand() {
return strand;
}
public Strand getSecondOfPairStrand() {
return Strand.NONE;
}
public Strand getReadStrand() {
return isNegativeStrand() ? Strand.NEGATIVE : Strand.POSITIVE;
}
@Override
public void finish() {
}
@Override
public boolean isPrimary() {
return true;
}
@Override
public boolean isSupplementary() {
return false;
}
}